[gmx-users] error while equilibration
I am trying to simulate RNA in water. I have minimized the system with steepest Decent for 2000 steps and then with Conjugate gradient for till the energy coverage reaches to 100 Kj/mol. But when I am trying to equilibrate it I am getting following error --- Program mdrun, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/mdlib/pme.c, line: 538 Fatal error: 11 particles communicated to PME node 3 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- My nvt.mdp file contain title = RNA complex NVT equilibration define = -DPOSRES ; position restrain ; Run parameters integrator = md; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps energygrps = RNA SOL NA ; Bond parameters continuation= no; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 0.9 ; short-range neighborlist cutoff (in nm) rcoulomb= 0.9 ; short-range electrostatic cutoff (in nm) rvdw= 1.4 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = RNA SOL NA ; two coupling groups - more accurate tau_t = 0.1 0.1 0.1 ; time constant, in ps ref_t = 310 310 310; reference temperature, one for each group, in K ; Pressure coupling pcoupl = no; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 310 ; temperature for Maxwell distribution gen_seed= -1; generate a random seed Please tell me where I am doing wrong. -- Ananya Chatterjee, Senior Research Fellow (SRF), Department of biological Science, IISER-Kolkata. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to perform simulation between initial and final structures
Dear All, I am working in a GTPase protein and I have two PDB structures of my protein in GTP-bound and GDP-bound state which have two different conformations. Now I want to perform simulation in between the structures to see how the conformational change is taking place. So is it possible to perform simulation keeping the initial and the final structure fixed. Please kindly provide me the procedure. Thank you in advance, -- Ananya Chatterjee, Senior Research Fellow (SRF), Department of biological Science, IISER-Kolkata. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Validation of molecular dynamic simulation results
On Tue, 11 Feb 2014 09:05:19 +0100, João Henriques wrote: Dear Ananya, Shouldn't this be something you already had in mind even before attempting to simulate? Usually, a simulation is a means to an end. What is your end, ie. what made you do this simulation? The motivation behind your simulation is usually what will determine what type of validation it requires. Sure, there are quasi-standard analysis and sanity checks that one almost always uses to ensure the simulation is relevant, but you can find those in any given MD tutorial available online. For this, Google is your friend and you also have quite popular tutorials such as Justin's for example: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/ I suggest you sit down and think a bit about what are you attempting to achieve with your simulation. Pinpoint what type of analysis you need and then take a careful look at the Gromacs manual. There you will find all you need to know about the analysis tools available to you. They're not guaranteed to cover all your needs, but they usually more than suffice in providing what most researchers need to validate their simulations. Best regards, João On Tue, Feb 11, 2014 at 8:02 AM, ananyachatterjee ananyachatter...@iiserkol.ac.in wrote: Hello everyone, I have done a set of molecular dynamic simulation of my protein and its mutated structure, now please tell me how should I validate the simulation results or structures. Whether I can reproduce the same simulations. Thank you in advance -- Ananya Chatterjee, Senior Research Fellow (SRF), Department of biological Science, IISER-Kolkata. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. Dear João, Thank you for your reply, I was intended to seen the difference in molecular movement of my protein upon mutation. My protein is a GTPase protein and I have done simulation in presence of GTP, GDP and GDP+Pi for both the wild type and the mutated protein. Then I have done principle component analysis and RMSD RMSF comparison of the trajectories. Now I want to check the authenticity of the set of simulation and whether they can be reproduce to validate my results. Please kindly help me in this regard. -- Ananya Chatterjee, Senior Research Fellow (SRF), Department of biological Science, IISER-Kolkata. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Validation of molecular dynamic simulation results
Dear Sir, My protein contains two domain and upon GTP hydrolysis, the protein under goes conformational change and it shows inter-domain movement. I did few biochemical test which showed me that the upon a mutation in the conserved residue (which is localed in the chain connecting the two domain)the GTPase activity is reduced and also it has effected the cell growth. Now to see whether the mutation is some how effecting the inter domain movement of the protein(which is a important property of the protein for it function) I performed the simulations keeping the parameters close to the biochemical experiments(like con. of ions, temp. etc) . Now when I presented my work in a conference people asked me about its authenticity, how much close it is to the reality and whether it is reproducible. I want to know how to verify my simulations. Thanks in advance On Tue, 11 Feb 2014 11:24:53 +0100, João Henriques wrote: Dear Ananya, Sorry but I don't understand what you're saying. What do you mean by molecular movement of my protein? Do you mean diffusion? Please be more specific. You also mention authenticity, but I don't think that's what you meant... You have done PCA, RMSD and RMSF analyses. That's nice and all, but do you have a reason for doing them? What I meant with my previous email is that *there is no fixed recipe that one must always follow in order to validate their simulations*. The analyses your simulation requires in order to be validated depend on the simulation purpose and what experimental data you have to compare them to. Take this overly simplistic example: Imagine I've performed a simple protein in water MD simulation. The protein is well behaved (stable native structure) and there is a high resolution experimental structure of it. Radius of gyration, RMSD, RMSF and DSSP analyses would be good candidates to show whether my force field, settings and parameters are adequate or not in maintaining the well known native 3D structure. Like I said before, you're the one that must be familiar with your system, simulation and overall project aim. I am happy to help you in identifying the tool you need to perform a certain analysis/study or even helping understanding any error or problem with it. However I cannot do your own work in identifying what needs to be done and where you're heading. Best regards, João On Tue, Feb 11, 2014 at 9:46 AM, ananyachatterjee ananyachatter...@iiserkol.ac.in wrote: On Tue, 11 Feb 2014 09:05:19 +0100, João Henriques wrote: Dear Ananya, Shouldn't this be something you already had in mind even before attempting to simulate? Usually, a simulation is a means to an end. What is your end, ie. what made you do this simulation? The motivation behind your simulation is usually what will determine what type of validation it requires. Sure, there are quasi-standard analysis and sanity checks that one almost always uses to ensure the simulation is relevant, but you can find those in any given MD tutorial available online. For this, Google is your friend and you also have quite popular tutorials such as Justin's for example: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/ I suggest you sit down and think a bit about what are you attempting to achieve with your simulation. Pinpoint what type of analysis you need and then take a careful look at the Gromacs manual. There you will find all you need to know about the analysis tools available to you. They're not guaranteed to cover all your needs, but they usually more than suffice in providing what most researchers need to validate their simulations. Best regards, João On Tue, Feb 11, 2014 at 8:02 AM, ananyachatterjee ananyachatter...@iiserkol.ac.in wrote: Hello everyone, I have done a set of molecular dynamic simulation of my protein and its mutated structure, now please tell me how should I validate the simulation results or structures. Whether I can reproduce the same simulations. Thank you in advance -- Ananya Chatterjee, Senior Research Fellow (SRF), Department of biological Science, IISER-Kolkata. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. Dear João, Thank you for your reply, I was intended to seen the difference in molecular movement of my protein upon mutation. My protein is a GTPase protein and I have done simulation in presence of GTP, GDP and GDP+Pi for both the wild type and the mutated protein. Then I have done principle component analysis and RMSD RMSF comparison of the trajectories. Now I want to check the authenticity of the set of simulation and whether they can be reproduce to validate my results
[gmx-users] Validation of molecular dynamic simulation results
Hello everyone, I have done a set of molecular dynamic simulation of my protein and its mutated structure, now please tell me how should I validate the simulation results or structures. Whether I can reproduce the same simulations. Thank you in advance -- Ananya Chatterjee, Senior Research Fellow (SRF), Department of biological Science, IISER-Kolkata. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
